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Markov model

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https://www.readbyqxmd.com/read/28087821/selection-of-first-line-therapy-in-multiple-sclerosis-using-risk-benefit-decision-analysis
#1
David Bargiela, Matthew T Bianchi, M Brandon Westover, Lori B Chibnik, Brian C Healy, Philip L De Jager, Zongqi Xia
OBJECTIVE: To integrate long-term measures of disease-modifying drug efficacy and risk to guide selection of first-line treatment of multiple sclerosis. METHODS: We created a Markov decision model to evaluate disability worsening and progressive multifocal leukoencephalopathy (PML) risk in patients receiving natalizumab (NTZ), fingolimod (FGL), or glatiramer acetate (GA) over 30 years. Leveraging publicly available data, we integrated treatment utility, disability worsening, and risk of PML into quality-adjusted life-years (QALYs)...
January 13, 2017: Neurology
https://www.readbyqxmd.com/read/28087663/evolution-and-structural-diversification-of-nictaba-like-lectin-genes-in-food-crops-with-a-focus-on-soybean-glycine-max
#2
Sofie Van Holle, Pierre Rougé, Els J M Van Damme
BACKGROUND AND AIMS: The Nictaba family groups all proteins that show homology to Nictaba, the tobacco lectin. So far, Nictaba and an Arabidopsis thaliana homologue have been shown to be implicated in the plant stress response. The availability of more than 50 sequenced plant genomes provided the opportunity for a genome-wide identification of Nictaba-like genes in 15 species, representing members of the Fabaceae, Poaceae, Solanaceae, Musaceae, Arecaceae, Malvaceae and Rubiaceae. Additionally, phylogenetic relationships between the different species were explored...
January 12, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28087548/early-lens-extraction-with-intraocular-lens-implantation-for-the-treatment-of-primary-angle-closure-glaucoma-an-economic-evaluation-based-on-data-from-the-eagle-trial
#3
Mehdi Javanbakht, Augusto Azuara-Blanco, Jennifer M Burr, Craig Ramsay, David Cooper, Claire Cochran, John Norrie, Graham Scotland
OBJECTIVE: To investigate the cost-effectiveness of early lens extraction with intraocular lens implantation for the treatment of primary angle closure glaucoma (PACG) compared to standard care. DESIGN: Cost-effectiveness analysis alongside a multicentre pragmatic two-arm randomised controlled trial. Patients were followed-up for 36 months, and data on health service usage and health state utility were collected and analysed within the trial time horizon. A Markov model was developed to extrapolate the results over a 5-year and 10-year time horizon...
January 13, 2017: BMJ Open
https://www.readbyqxmd.com/read/28086791/identification-of-functional-enolase-genes-of-the-silkworm-bombyx-mori-from-public-databases-with-a-combination-of-dry-and-wet-bench-processes
#4
Akira Kikuchi, Takeru Nakazato, Katsuhiko Ito, Yosui Nojima, Takeshi Yokoyama, Kikuo Iwabuchi, Hidemasa Bono, Atsushi Toyoda, Asao Fujiyama, Ryoichi Sato, Hiroko Tabunoki
BACKGROUND: Various insect species have been added to genomic databases over the years. Thus, researchers can easily obtain online genomic information on invertebrates and insects. However, many incorrectly annotated genes are included in these databases, which can prevent the correct interpretation of subsequent functional analyses. To address this problem, we used a combination of dry and wet bench processes to select functional genes from public databases. RESULTS: Enolase is an important glycolytic enzyme in all organisms...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28078600/net-budgetary-impact-of-ferric-citrate-as-a-first-line-phosphate-binder-for-the-treatment-of-hyperphosphatemia-a-markov-microsimulation-model
#5
Steven M Brunelli, Scott P Sibbel, David Van Wyck, Amit Sharma, Andrew Hsieh, Glenn M Chertow
Ferric citrate (FC) has demonstrated efficacy as a phosphate binder and reduces the requirements for erythropoiesis-stimulating agents (ESAs) and intravenous (IV) iron in dialysis patients. We developed a net budgetary impact model to evaluate FC vs. other phosphate binders from the vantage of a large dialysis provider. We used a Markov microsimulation model to simulate mutually referential longitudinal effects between serum phosphate and phosphate binder dose; categories of these defined health states. Health states probabilistically determined treatment attendance and utilization of ESA and IV iron...
January 11, 2017: Drugs in R&D
https://www.readbyqxmd.com/read/28078557/cost-effectiveness-analysis-of-universal-screening-for-carbapenemase-producing-enterobacteriaceae-in-hospital-inpatients
#6
L Lapointe-Shaw, T Voruganti, P Kohler, H-H Thein, B Sander, A McGeer
The purpose of this study was to assess the cost-effectiveness of screening all hospital inpatients for carbapenemase-producing Enterobacteriaceae (CPE) at the time of hospital admission, compared to not screening, from a US hospital perspective. We used a linked transmission/Markov model to compare outcomes for a typical hospitalized medical patient, from a community with a colonization prevalence of 0.05%. Outcomes were number of colonized patients, CPE-related clinical infections and deaths, expected quality-adjusted life years (QALYs), cost, and the incremental cost-effectiveness ratio (ICER)...
January 11, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28078461/cost-effectiveness-of-prophylactic-appendectomy-a-markov-model
#7
Karina Newhall, Benjamin Albright, Anna Tosteson, Elissa Ozanne, Thadeus Trus, Philip P Goodney
BACKGROUND: Appendectomy is the most common emergency surgery performed in the USA. Removal of a non-inflamed appendix during unrelated abdominal surgery (prophylactic or incidental appendectomy) can prevent the downstream risks and costs of appendicitis. It is unknown whether such a strategy could be cost saving for the health system. METHODS: We considered hypothetical patient cohorts of varying ages from 18 to 80, undergoing elective laparoscopic abdominal and pelvic procedures...
January 11, 2017: Surgical Endoscopy
https://www.readbyqxmd.com/read/28076801/msmbuilder-statistical-models-for-biomolecular-dynamics
#8
Matthew P Harrigan, Mohammad M Sultan, Carlos X Hernández, Brooke E Husic, Peter Eastman, Christian R Schwantes, Kyle A Beauchamp, Robert T McGibbon, Vijay S Pande
MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov state models (MSMs), a class of models that has gained favor among computational biophysicists. In addition to both well-established and newer MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models and time-structure based independent component analysis...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076429/turning-simulation-into-estimation-generalized-exchange-algorithms-for-exponential-family-models
#9
Maarten Marsman, Gunter Maris, Timo Bechger, Cees Glas
The Single Variable Exchange algorithm is based on a simple idea; any model that can be simulated can be estimated by producing draws from the posterior distribution. We build on this simple idea by framing the Exchange algorithm as a mixture of Metropolis transition kernels and propose strategies that automatically select the more efficient transition kernels. In this manner we achieve significant improvements in convergence rate and autocorrelation of the Markov chain without relying on more than being able to simulate from the model...
2017: PloS One
https://www.readbyqxmd.com/read/28076183/markov-influence-diagrams
#10
Francisco J Díez, Mar Yebra, Iñigo Bermejo, Miguel A Palacios-Alonso, Manuel Arias Calleja, Manuel Luque, Jorge Pérez-Martín
Markov influence diagrams (MIDs) are a new type of probabilistic graphical model that extends influence diagrams in the same way that Markov decision trees extend decision trees. They have been designed to build state-transition models, mainly in medicine, and perform cost-effectiveness analyses. Using a causal graph that may contain several variables per cycle, MIDs can model various patient characteristics without multiplying the number of states; in particular, they can represent the history of the patient without using tunnel states...
February 2017: Medical Decision Making: An International Journal of the Society for Medical Decision Making
https://www.readbyqxmd.com/read/28075249/cost-effectiveness-analysis-of-as04-adjuvanted-human-papillomavirus-16-18-vaccine-compared-with-human-papillomavirus-6-11-16-18-vaccine-in-the-philippines-with-the-new-2-dose-schedule
#11
Maria Julieta Germar, Carrie Purugganan, Ma Socorro Bernardino, Benjamin Cuenca, Y-Chen Chen, Xiao Li, Georges Van Kriekinge, I-Heng Lee
Cervical cancer (CC) is the second leading cause of cancer death among Filipino women. Human papillomavirus (HPV) vaccination protects against CC. Two vaccines (AS04-HPV-16/18 and 4vHPV) are approved in the Philippines; they were originally developed for a 3-dose (3 D) administration and have recently been approved in a 2-dose schedule (2 D). This study aims to evaluate the cost-effectiveness and budget impact of HPV vaccination of 13-year-old Filipino girls, in addition to current screening, in the new 2 D schedule...
January 11, 2017: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/28070777/breast-ultrasound-image-segmentation-a-survey
#12
REVIEW
Qinghua Huang, Yaozhong Luo, Qiangzhi Zhang
PURPOSE: Breast cancer is the most common form of cancer among women worldwide. Ultrasound imaging is one of the most frequently used diagnostic tools to detect and classify abnormalities of the breast. Recently, computer-aided diagnosis (CAD) systems using ultrasound images have been developed to help radiologists to increase diagnosis accuracy. However, accurate ultrasound image segmentation remains a challenging problem due to various ultrasound artifacts. In this paper, we investigate approaches developed for breast ultrasound (BUS) image segmentation...
January 9, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28068242/cost-effectiveness-analysis-of-preoperative-versus-postoperative-radiation-therapy-in-extremity-soft-tissue-sarcoma
#13
Xuanlu M Qu, Alexander V Louie, Jonathan Ashman, Nabil Wasif
PURPOSE: Surgery combined with radiation therapy (RT) is the cornerstone of multidisciplinary management of extremity soft tissue sarcoma (STS). Although RT can be given in either the preoperative or the postoperative setting with similar local recurrence and survival outcomes, the side effect profiles, costs, and long-term functional outcomes are different. The aim of this study was to use decision analysis to determine optimal sequencing of RT with surgery in patients with extremity STS...
February 1, 2017: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/28067598/why-so-narrow-distribution-of-anti-sense-regulated-type-i-toxin-antitoxin-systems-compared-to-type-ii-and-type-iii-systems
#14
Dorien S Coray, Nicole E Wheeler, Jack A Heinemann, Paul P Gardner
Toxin-antitoxin (TA) systems are gene modules that appear to be horizontally mobile across a wide range of prokaryotes. It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs that rely on direct toxin-antitoxin binding but no direct comparisons have been made. We searched for type I, II and III toxin families using iterative searches with profile hidden Markov models across phyla and replicons. The distribution of type I toxin families were comparatively narrow, but these patterns weakened with recently discovered families...
January 9, 2017: RNA Biology
https://www.readbyqxmd.com/read/28066502/a-correlated-binary-model-for-ignorable-missing-data-application-to-rheumatoid-arthritis-clinical-data
#15
Francis Erebholo, Victor Apprey, Paul Bezandry, John Kwagyan
Incomplete data are common phenomenon in research that adopts the longitudinal design approach. If incomplete observations are present in the longitudinal data structure, ignoring it could lead to bias in statistical inference and interpretation. We adopt the disposition model and extend it to the analysis of longitudinal binary outcomes in the presence of monotone incomplete data. The response variable is modeled using a conditional logistic regression model. The nonresponse mechanism is assumed ignorable and developed as a combination of Markov's transition and logistic regression model...
April 2016: Journal of Data Science: JDS
https://www.readbyqxmd.com/read/28065836/learning-effective-connectivity-from-fmri-using-autoregressive-hidden-markov-model-with-missing-data
#16
Shilpa Dang, Santanu Chaudhury, Brejesh Lall, Prasun Kumar Roy
BACKGROUND: Effective connectivity (EC) analysis of neuronal groups using fMRI delivers insights about functional-integration. However, fMRI signal has low-temporal resolution due to down-sampling and indirectly measures underlying neuronal activity. NEW METHOD: The aim is to address above issues for more reliable EC estimates. This paper proposes use of autoregressive hidden Markov model with missing data (AR-HMM-md) in dynamically multi-linked (DML) framework for learning EC using multiple fMRI time series...
January 5, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28065628/health-utility-of-early-hemiarthroplasty-vs-delayed-total-hip-arthroplasty-for-displaced-femoral-neck-fracture-in-elderly-patients-a-markov-model
#17
Lauren M Uhler, W Randall Schultz, Austin D Hill, Karl M Koenig
BACKGROUND: Treatment for femoral neck fracture among patients aged 65 years or older varies, with many surgeons preferring hemiarthroplasty (HA) over total hip arthroplasty (THA). There is evidence that THA may lead to better functional outcomes, although it also carries greater risk of mortality and dislocation rates. METHODS: We created a Markov decision model to examine the expected health utility for older patients with femoral neck fracture treated with early HA (performed within 48 hours) vs delayed THA (performed after 48 hours)...
December 14, 2016: Journal of Arthroplasty
https://www.readbyqxmd.com/read/28063376/a-comprehensive-non-invasive-framework-for-diagnosing-prostate-cancer
#18
Islam Reda, Ahmed Shalaby, Mohammed Elmogy, Ahmed Abou Elfotouh, Fahmi Khalifa, Mohamed Abou El-Ghar, Ehsan Hosseini-Asl, Georgy Gimel'farb, Naoufel Werghi, Ayman El-Baz
Early detection of prostate cancer increases chances of patients' survival. Our automated non-invasive system for computer-aided diagnosis (CAD) of prostate cancer segments the prostate on diffusion-weighted magnetic resonance images (DW-MRI) acquired at different b-values, estimates its apparent diffusion coefficients (ADC), and classifies their descriptors - empirical cumulative distribution functions (CDF) - with a trained deep learning network. To segment the prostate, an evolving geometric (level-set-based) deformable model is guided by a speed function depending on intensity attributes extracted from the DW-MRI with nonnegative matrix factorization (NMF)...
December 23, 2016: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28062446/phmm-tree-phylogeny-of-profile-hidden-markov-models
#19
Luyang Huo, Han Zhang, Xueting Huo, Yasong Yang, Xueqiong Li, Yanbin Yin
: Protein families are often represented by profile hidden Markov models (pHMMs). Homology between two distant protein families can be determined by comparing the pHMMs. Here we explored the idea of building a phylogeny of protein families using the distance matrix of their pHMMs. We developed a new software and web server (pHMM-tree) to allow four major types of inputs: (i) multiple pHMM files, (ii) multiple aligned protein sequence files, (iii) mixture of pHMM and aligned sequence files and (iv) unaligned protein sequences in a single file...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28060834/estimating-the-cost-effectiveness-of-one-time-screening-and-treatment-for-hepatitis-c-in-korea
#20
Do Young Kim, Kwang-Hyub Han, Byungyool Jun, Tae Hyun Kim, Sohee Park, Thomas Ward, Samantha Webster, Phil McEwan
BACKGROUND AND AIMS: This study aims to investigate the cost-effectiveness of a one-time hepatitis C virus (HCV) screening and treatment program in South Korea where hepatitis B virus (HBV) prevails, in people aged 40-70, compared to current practice (no screening). METHODS: A published Markov model was used in conjunction with a screening and treatment decision tree to model patient cohorts, aged 40-49, 50-59 and 60-69 years, distributed across chronic hepatitis C (CHC) and compensated cirrhosis (CC) health states (82...
2017: PloS One
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